A Logical Decision
by Roxanne15927
Summary: One month after the Fall, Sherlock Holmes, now Khan, has to make a decision concerning the fate of his best friend. No slash.
1. A Second Farewell

**Hi! Well, this is my first time ever publishing a crossover story, so I hope you all like it! Please enjoy and review!  
**

A Logical Decision

"We will leave the decision up to you. You have one hour."

There was the sound of footsteps leaving the room, the slam of the heavy, steel door, and he was alone.

His decision_. His_ decision.

He chuckled drily to himself. Nothing had been ultimately his decision since the day he jumped. His eyebrows creased as unbidden memories rose to the surface. In the past few months, it had been all too easy to push them down, even easier than it had been before ('before' was the only word that he would attribute to his past). In fact, he rarely thought about his before, if at all. The quickness, the raging, wild system of his genetically enhanced brain, frighteningly and impressively faster than his mind from before, the staggeringly vast learning abilities and expanded storage of information left little, if any room for memories of before. It was almost as if that life, that life from before had never existed, just a fleeting, brief amount of time. His mind, which in the life of before he had described a mind palace, was now so much more than a useless little palace; it was a universe. Logically, he knew there was nothing to be gained by remembering life from before, so it was pushed away into the farthest, dustiest corners of his mind-but it was still irritatingly present.

And now he was being asked to decide the fate of someone from his 'before'-the one person he had purposely not allowed himself to even entertain a thought of.

Because with this person's face, his name-it brought pain, it brought longing, and it brought the oddest feeling of all- desperate hope.

Dr. Watson's information automatically popped up in his mind like words on a computer screen, scrolling through his mind's eye.

_Dr. John Hamish Watson_

_Captain, Fifth Northumberland Fusiliers _

_42 years old_

_Date of birth: September 8, 1971_

_Marital status: Unmarried_

_Family-_

_Father: Duncan Watson, Mother: Kate Brown Watson._

_Sibling(s): Harriet Watson_

_Current employment: None_

He frowned. Why would any of this pointless information-why would this man mean anything?

_Dr. John Hamish Watson_

_John Hamish Watson_

_John Watson_

_John_

_John_

_Flatmate_

_Colleague _

_Friend_

_Best friend_

Friend…that was the word that puzzled him the most.

He didn't have friends. There was literally no one that he needed in his life. There was not a single person that could offer him something he did not already have, he had no weaknesses.

But yet-there was still this pull, something tangible moving him towards this John Watson. Out of any person he knew from before, he could call up memories of this man the quickest, his voice, his face, and most dominantly, this deeply cemented _need_ to protect him, to make sure he was happy and well.

But as he had been told so many times since the beginning of his process-everything, everyone from 'before' did not matter. They were tiny and insignificant in comparison to the now, and thinking about it was a valuable waste of time.

Despite knowing this, this was just one thing he could not help.

He knew that he had jumped from a building to save John Watson, to ensure John's safety, and his happiness. He knew that though his mind before was pathetic compared to his mind now, he knew even before he had had a brain superior to most. If he had that even then, even with his highly intelligent brain had still decided to jump for a single man, he reasoned now that he must have been, to say the least, enormously important.

Which made his decision now all the more difficult.

When he had jumped, his plan,-which he saw now had a ghastly amount of flaws-had gone horribly wrong. He did, technically speaking, die-until someone from the now stepped in and changed everything.

With the consent of his brother from before, he became a subject of a completely secret underground experiment, the first subject of the operation to succeed.

Sherlock Holmes died that day-and Khan was born.

Since then, he had been living in this facility, with the 'testers'-he found it of no importance to learn any of their names-adjusting to his new, superhuman body. His existence thus far had been dull-he was not allowed out of the facility, his time was spent, for the lack of a better word, training.

Yesterday, he had been given a choice to enter into a hypersleep-waiting for a time where technology would be more advanced, where his abilities would be useful, not overwhelming to the natural world-the world at present was literally not prepared for his genius and his strength.

The decision had been a simple one. A week from today, he would be put to sleep, not to be awakened until it was a "better time".

Until he remembered his friend from before, John. The testers thought of this not long after he did, and they gave him a choice-they could bring John Watson in, perform the same experiment, and put him into hypersleep along with Khan-and they both would be awakened at the same time, both together, and both equals-or they could leave him be.

Khan's first instinct was to say yes-bring in John Watson, bring him his friend-but then…there was so much more he still had to consider.

Was it fair to rip John Watson away from his life, force him into becoming a science experiment, to say goodbye to everything he knew?

No. It wasn't fair.

And who was to say that his John Watson from before would be the same after the experiment-Khan knew that he was hardly the same person he was from before-for Khan himself, the name and persona of Sherlock Holmes seemed as foreign to him as a stranger on the streets. Would he truly have returned to him his friend from before? Or would he be delivered a stranger?

Logically, he knew he could not expect John Watson to be returned to him one hundred percent perfect. He knew that there was an almost certain chance that he could be receiving an enemy, what with his military history, his personality, and strength-John Watson, already a force to be reckoned with, would be absolutely lethal after this experiment, a weapon of complete destruction. And once done-there would be no going back.

There was no need to check the time-exactly fifty six minutes, and thirty three seconds had passed since the testers had left the room.

It was then he knew he needed no more time-his decision was made.

John Watson would die.

Not today, no-but he would go on and live his life, go on without Sherlock, go on alone-and in an expected amount of time, John would die-and Sherlock-

Khan would continue to live.

Alone.

In the end, though, it would be the most logical decision.

###

"Please proceed to room 221 in fifteen minutes."

There was the sound of footsteps again, and the door shut.

Khan had made his decision.

In fifteen minutes, he would enter into hypersleep, and everything from before would completely, truly be deleted-having absolutely no relevance.

But there was one last thing that needed to be done as Sherlock Holmes.

Tester #3's laptop was placed in front of him. A video feed had been brought up on the screen, ready to record. After a moment, making sure he was alone, he leaned forward. "Begin recording."

The computer beeped to show that it had understood, and a red light flashed.

"January 3rd, 2014," Khan began. "To Dr. John Hamish Watson, from Sherlock Holmes."

The computer beeped three times, and Khan continued.

"John," he said, surprised by the emotion that came to his voice when he spoke the name-"When I left-I always expected to come back." He hadn't expected to plunge so quickly into this speech, but it seemed appropriate, and the words began to come, faster than he thought they would have. This had to be done, and had to be said.

"I always expected to come back and tell you how much you meant to me. But now-now I'll never get that chance. I can't tell you what happened to me, and I can't tell you why, but I just want you to know, wherever you are-that everything I did-" he choked on the sudden, rising emotion, his eyes burning with unshed moisture-"And everything I do-I do for you, because you are the only thing in my life that ever _truly_ mattered." He swallowed hard, and went on. "That-that is why I left, and it is why I am making the decision to leave you now. And so it is with a heavy heart, that I once again bid you farewell. Goodbye, John. You were, and are the best man that I have ever known, and your friendship meant more to me than you will ever know."

He closed his eyes, and then opened them again.

"Sherlock Holmes is dead. My name…is Khan."

He gave a curt nod.

"End recording."


	2. A Plan Disturbed

Year 2259

One week, four days since Khan had been awakened from the hypersleep. Though 72 other test subjects just like him were meant to be awakened at the same time, only Khan was revived.

The man who had awoken him was not one of the testers that Khan remembered from so many years ago-before entering the hypersleep, he had been told who to expect-and this man was definitely not who he was supposed to expect.

His name was Marcus, Admiral Marcus, and it quickly became apparent that he had an ulterior motive for waking up Khan-and Khan had no choice but to comply.

Yes, Khan was stronger, he was faster, he was smarter-but Marcus had the advantage: the seventy two other men and women who had been in hypersleep with him were under Marcus's control-if Khan did not cooperate with the admiral's plan, the lives of those men and women would be taken.

He agreed-his reasons, simply put-it's what John would do.

He marveled at the fact that after all these years, he still thought of what his friend John would do. But, as he had promised him in his video farewell so many years ago-everything Khan did and everything he would do would be for John. It was the only way to keep John's memory alive.

In this new (though he could hardly call it new anymore) body, he experienced emotions differently than he had done before-along with everything else that had come with his new body, they came harder, quicker, and with even more vengeance. There was no distancing himself from feelings anymore-but in John's case, that was one thing Khan-Sherlock? had never been able to do.

Khan had complied with Marcus' plan long enough-it was time to initiate a plan of his own.

###

Year 2015

_"Sherlock Holmes is dead. My name…is Khan."_

_"End recording."_

John didn't know how many times he replayed the video, but he knew it was enough times that he had every word memorized, every gesture, and every motion.

His mind was spinning, his heart was racing, and the world was tilting, a strange tingling going up and down his arms.

Sherlock was alive.

Sherlock was _alive_.

John was feeling too many things at once, too many memories were whirling through his mind, too much sadness, too much anger, just too much of everything. There was only one other time where he remembered feeling like this-and after a year it was still much too difficult to think about. This whole year-this whole year of grieving, of suffering, of pain-it had all been for nothing. His best friend had been alive this entire time-but as something else entirely.

It was Sherlock in the video, he knew that for certain, but he looked-different, for lack of a better word.

It was his friend, though-alive and well.

But he had said goodbye-

Again.

John's heart was heavy with the weight of his best friend's second farewell, the back of his eyes burning with unshed tears. It hurt all over-he couldn't remember feeling an emotional pain this physical since-

Since that first time.

"John?" Mycroft's voice came from the doorway, sounding irritatingly sympathetic.

"You knew, didn't you?" Forcing out the words was like moving through quicksand. "You…you _knew_."

"Of course," Mycroft responded coolly, his voice still tinged with that annoying sympathy. "His condition was critical. He would have died otherwise."

That was the moment it all snapped.

"He still died!" John roared, getting up and whirling around to face Mycroft. "He still died, the day he jumped from that rooftop, Sherlock Holmes _died_. That wasn't Sherlock. That's Khan!" The word tasted foreign and strange on his tongue, and he hated it. He hated that name.

Khan-who was Khan? He wasn't John's flatmate, he wasn't John's partner, he wasn't John's best friend-this Khan _shouldn't_ matter to him.

"This doesn't change anything! It changes nothing!" John continued, still shouting at Mycroft, who was taking this all as he always did-with an indifferent, calm expression on his face. "If anything, all you've done-" John's voice broke unexpectedly-"all you've done is kill him a second time."

Without thinking about it, he pulled up a chair and sat down heavily, his body sagging from the weight of this new pain the video had inflicted on him.

Mycroft was quiet for a moment, then he finally spoke. "Despite what you seem to think, I did not show you this to hurt you. I am simply doing what's best for you, and for my brother. After all, he wanted you to see this video."

"How is this best?" John demanded. "He sent me this video a year ago-why did you wait to show me until now?"

"Because a year ago, the offer I am about to present you was not available to me, and I fully believe you would have asked for it then. I needed time."

"What are you talking about? What offer?"

"One year ago, Sherlock was given a choice-to allow you to join him as the next genetically engineered superhuman, or allow you to go on with your life as normal. As you can probably tell already, he chose the latter."

Something clenched uncomfortably in John's chest. "Why would he choose-" He trailed off, realizing the answer before Mycroft had a chance to voice it.

"I expect he meant to protect you," the elder Holmes observed. "At the time that video was made, he was preparing to enter into hypersleep. Had he made the decision to bring you in, you would have done the same, against your will and without your consent. Your life here would have ended permanently without a chance to resist. He understood the costs, and he clearly did not want you to have to pay them."

John shook his head, getting up from his chair and walking up to Mycroft. "I'll do it."

Mycroft's eyebrow furrowed, puzzled. "Do what?"

John laughed, though humorlessly. "It's obvious, isn't it? You're giving me the choice to undergo the same operation that Sherlock did."

Mycroft raised an eyebrow, looking surprised and mildly impressed. "I see your time with my brother was not entirely wasted." He gave a short nod, and stepped closer to John. "But if you choose this, I have to warn you, you will never be able to return."

"I understand," John responded calmly.

"There is a very strong chance that you may not even survive the operation, and there is a strong chance that you may not ever be reunited with Sherlock. You must understand that undergoing the operation does not guarantee anything."

"I understand the costs," John said, parroting back Mycroft's words from earlier, "and I am willing to pay them. I want the operation, Mycroft. I am done letting Sherlock try to protect me. It's time I took my own life into my hands."

He moved past Mycroft, and to the door. He stopped and turned, looking back. "And I'm not looking for Sherlock," he said. "I'm looking for Khan."

###

Khan moved about the torpedoes, checking each one carefully. It had taken time, distancing the process over a period of four days, but he had successfully put all 72 men, women and children into his self designed torpedoes. It had taken a laughably short time to lift the pitiful security Marcus had on the subjects, and an even easier time to move the subjects to the torpedoes, all under the nose of Admiral Marcus himself. Of course, he had to work at night, but it wasn't a problem. He felt that he worked better in the nighttime anyway.

"Good work, Mr. Harrison."

Khan didn't even need to turn to know who it was. "Admiral."

This wasn't right, Marcus wasn't even supposed to be on the ship-

"I knew you were up to something," Marcus spoke again, his voice echoing through the chamber. "I just didn't know what. Proud of yourself, are you?"

Now Khan did turn to look at him, his face set in a nonchalant expression. "Perhaps."

"Excellent," the admiral replied sarcastically. "So am I." He moved forward, walking along the line of torpedoes. "You saved me a lot of work, you know. Oh no," he continued, catching the brief perplexed expression that must have come to Khan's face, "I'm not going to dismantle all your hard work, no no _no_, I could never do that."

Khan remained stone still, watching the admiral carefully.

"You don't know it yet, but you have actually saved me a lot of trouble," Marcus continued. "Much easier to dispose of this way. Thank you…but, there is just one thing."

"What is that?" Khan asked.

"You've forgotten one," Marcus responded. "Go on and see for yourself." He gestured to the rows of empty cyrotubes behind them.

Khan's eyes narrowed slightly. That definitely was not possible, he knew he had not missed even one of the 72 subjects, he had checked to make certain. The only way that he could have missed one would be-

If there was one more.

Ignoring Marcus, Khan turned and walked to the cyrotubes, going on even though he was aware that the admiral was following behind him. He saw it in moments, the one activated cyrotube glowing dimly in the darkness.

It was impossible, how was there a seventy third tube-?

They both stopped at the tube, though Khan did not look inside.

"Open it," Marcus commanded.

Khan knew the best course of action as of now was to do as he was told, as much as he hated to do it. He moved to do so, when Marcus interrupted. "And wake him up, while you're at it."

Khan's outstretched fingers curled in and out again, hanging above the mysterious tube.

After a moment's hesitation, he did as he was told. The panel slid open, the sound reverberating through the room, with an accompanying hiss.

Before either of them had a chance to look inside, the silence was ripped apart by the blaring siren of the alarm.

Marcus glanced once at Khan, and without another word took off running, which meant that whatever was happening was far more pressing than worrying about the location of his superhuman prisoner. The loud boom and the slight vibrating of the floor confirmed this as he turned to see the admiral disappear through the doorway. Even though he knew he should be preparing the last steps of his plan, his curiosity won out in moments. He stepped forward to look-

The tube was empty.

The tube was _empty_.

Marcus had tricked him. It had been a distraction, a distraction from finishing his plan, and Khan had fallen for it.

He whirled back around to the torpedoes, and the next thing he knew he was reeling backwards from a powerful punch that had seemingly come out of nowhere, his cheek on fire from the blow. It was all the more surprising because ever since he underwent the operation, _nothing_, not one blow of any kind had hurt, in fact, each one had been completely and utterly laughable.

"You idiot. You, stupid, _bloody _idiot!" A harsh but oddly familiar voice came from his right, and Khan froze. He touched the already healing welt by his eye.

An old memory, as if on cue, immediately sounded in his mind.

_Somebody loves you... If I had to punch that face…I'd avoid your nose and teeth too._

There was only one person that Khan had ever known, that would take care to avoid his nose and teeth, only one person with _that_ voice-

He leapt to his feet, facing the man across from him. "John?"

It was John-but he was different, different than the man that Khan had known from before. His hair was shorter, much like what his hair would have looked like when he was in the military, his stance as ramrod straight as ever. He looked stronger, the muscles on his arms and body more defined. All of this brought Khan to one conclusion-John had undergone the same operation he had-but why? He had made sure that John would not follow him into this life-he didn't want this for him. At the same time, his heart was battering itself against his chest in frantic joy-it was John, the friend he was forced to say goodbye to so many years ago, the friend he believed he would never see again. He would take it all-John's anger, bitterness, and every blow-it was worth it to have him back.

John's expression was unreadable. "Hello, Sherlock. Oh no-you go by Khan now, is that right?" A line creased by John's eye. He was angry.

"John...you have every right to-"

The next thing Khan knew, he was reeling backwards from another blow.

"Don't tell me what I have a right to do," John shouted, advancing on him, his eyes on fire. "You've made it perfectly clear that I don't get to decide what I need. It's your choice, isn't it? Oh come on," he continued, noticing the puzzled expression on Khan's face, "don't pretend like you don't know. St. Bart's, the entire fall, this-" He gestured to Khan- "This was all about _you_ deciding what _I_ need. You didn't need to do any of those things for me. I don't need you to protect me. That's my job." The alarm continued to blare on as John spoke, seeming to beep faster and in a more insistent manner, as if begging them both to just _go_-but neither of them paid it any attention.

"Don't-don't do this. I never had any intention of hurting you. All I wanted was to keep you safe, to protect you." Khan insisted. He had expected John to be furious, but somehow John's words were surprising him.

"I don't need you to protect me!" John responded furiously. "I didn't need your protection. What I needed, what I _really_ needed, was for you to be there, and-" He pointed at Khan- "You. Weren't."

"I did what was best!" Khan shouted back. "You weren't supposed to follow me."

"Of course I was going to follow you! What did you expect?" John threw his hands up into the air, his anger fading into exasperation. He swore softly. "Look at the two of us," he said bitterly. "We haven't seen each other for three hundred years and the first thing we do is argue."

Khan hesitated, unsure how to proceed. If he remembered correctly, dry humour always seemed to alleviate John's dark moods. Khan raised an eyebrow. "You started it."

"I-I started it?" John's voice was incredulous, but at the same time he sounded amused. He laughed, but it was a short, resentful one. "You're just the same, aren't you?"

It was difficult to place his tone, which Khan found puzzling. He remembered distinctly from before that as Sherlock, he was able to tell John's moods and tones effortlessly, but now-it was different. But what could he expect? They were both the same yet completely different people now. Their minds and bodies had been altered in irreversible ways-Khan would have to get used to the new John, and John would have to get used to Khan.

But then John laughed again, and it was brighter, and happier. "I missed you, you git."

John stepped forward, and in the next moment they were embracing, and he seemed to sag against Khan, as if he couldn't find the strength to hold himself up alone any longer.

Khan felt relief coursing through him, coupled with an overwhelming happiness that he had John back, and he was here and warm and alive and for that moment, nothing in the world could threaten that.

The serenity of the moment was shattered by an enormous booming sound, and both stepped away quickly.

"We need to get off this ship," Khan said. "Now."

"I was thinking the exact same thing," John said, a note of sarcasm tinging his voice.

Khan rolled his eyes. "Let's go, then, shall we?"

Together, the two men exited the chamber, side by side at last.

###

"I was discovered. I had no choice but to escape…alone."

Khan closed his eyes, the memories flashing through his mind.

If only they knew.

If only they knew what he really lost.

Captain Kirk and Mr. Spock, standing there, pretending they could empathize with his pain-certainly, they were not showing it, or at least pretending not to-but he could see it.

He wanted to scream at them, yell at them, make them _suffer _for his pain-

But not yet.

It wasn't time.

Oh, they would suffer-they would all pay for his pain.

Every last one.


End file.
